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-rw-r--r--DESCRIPTION4
-rw-r--r--R/drfit.R46
-rw-r--r--inst/doc/README.txt14
-rw-r--r--inst/doc/sampledata.xlsbin19456 -> 16896 bytes
-rw-r--r--inst/doc/sampledata2.csv33
-rw-r--r--man/drplot.Rd8
6 files changed, 92 insertions, 13 deletions
diff --git a/DESCRIPTION b/DESCRIPTION
index 2ff9517..1f7becb 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
Package: drfit
-Version: 0.04-52
-Date: 2005-12-22
+Version: 0.04-54
+Date: 2006-01-02
Title: Dose-response data evaluation
Author: Johannes Ranke <jranke@uni-bremen.de>
Maintainer: Johannes Ranke <jranke@uni-bremen.de>
diff --git a/R/drfit.R b/R/drfit.R
index 9184dc9..ac3ad3e 100644
--- a/R/drfit.R
+++ b/R/drfit.R
@@ -287,7 +287,8 @@ drfit <- function(data, startlogED50 = NA, chooseone=TRUE,
return(results)
}
-drplot <- function(drresults, data, dtype = "std", alpha = 0.95,
+drplot <- function(drresults, data,
+ dtype = "std", alpha = 0.95, ctype = "none",
path = "./", fileprefix = "drplot", overlay = FALSE,
postscript = FALSE, png = FALSE, bw = TRUE,
pointsize = 12,
@@ -301,16 +302,30 @@ drplot <- function(drresults, data, dtype = "std", alpha = 0.95,
unit <- "different units"
}
- # Get the plot limits on the x-axis (log of the dose)
+ # Get the plot limits on the x-axis (log of the dose) and y axis
if(is.data.frame(data)) {
- if (min(data$dose) == 0) {
- cat("At least one of the dose levels is 0 - this is not a valid dose.")
- } else {
- lld <- log10(min(data$dose))
+ nonzerodata <- subset(data,dose!=0)
+ nonzerodata$substance <- factor(nonzerodata$substance) # Get rid of pseudo substance names of controls
+ zerodata <- subset(data,dose==0)
+ nc <- length(zerodata$dose) # Number of control points
+ sdc <- sd(zerodata$response) # Standard deviation of control responses
+ controlconf <- sdc * qt((1 + alpha)/2, nc - 1) / sqrt(nc)
+ if (nc > 0) {
+ cat("There are ",nc,"data points with dose 0 (control values)\n")
+ cat("with a standard deviation of",sdc,"\n")
+ cat("and a confidence interval of",controlconf,"\n")
+ if (nc < 3) {
+ cat("\nThere are less than 3 control points, therefore their scatter\n")
+ cat("will not be displayed\n")
+ ctype = "none"
+ }
}
- lhd <- log10(max(data$dose))
- hr <- max(data$response)
- dsubstances <- levels(data$substance)
+ lld <- log10(min(nonzerodata$dose))
+ lhd <- log10(max(nonzerodata$dose))
+ hr <- max(nonzerodata$response)
+ if (ctype == "std") hr <- max(hr,1 + sdc)
+ if (ctype == "conf") hr <- max(hr,1 + controlconf)
+ dsubstances <- levels(nonzerodata$substance)
} else {
lld <- min(drresults[["logED50"]],na.rm=TRUE) - 2
lhd <- max(drresults[["logED50"]],na.rm=TRUE) + 2
@@ -349,7 +364,7 @@ drplot <- function(drresults, data, dtype = "std", alpha = 0.95,
# Plot the data either as raw data or as error bars
if(is.data.frame(data)) {
- splitted <- split(data,data$substance)
+ splitted <- split(nonzerodata,nonzerodata$substance)
# n is the index for the dose-response curves
n <- 0
if (bw) colors <- rep("black",length(dsubstances))
@@ -389,6 +404,17 @@ drplot <- function(drresults, data, dtype = "std", alpha = 0.95,
# factor has all levels, not
# only the ones tested with
# this substance
+
+ # Plot the control lines, if requested
+ if (ctype == "std") {
+ abline(h = 1 - sdc, lty = 2)
+ abline(h = 1 + sdc, lty = 2)
+ }
+ if (ctype == "conf") {
+ abline(h = 1 - controlconf, lty = 2)
+ abline(h = 1 + controlconf, lty = 2)
+ }
+
# Plot the data, if requested
if (dtype != "none") {
if (dtype == "raw") {
diff --git a/inst/doc/README.txt b/inst/doc/README.txt
new file mode 100644
index 0000000..10945d9
--- /dev/null
+++ b/inst/doc/README.txt
@@ -0,0 +1,14 @@
+This sample data is provided to show how dose-response data can be collected
+with a spreadsheet program like OpenOfficeCalc (sampledata.ods) or
+MS Excel (sampledata.xls) and exported to CSV (comma separated values) format.
+OpenOfficeCalc 2.0 (German version, decimal separator is ',') produces
+sampledata.csv which can be read in by
+
+ >sampledata <- read.csv('sampledata.csv',skip=2,dec=',')
+
+and MS Excel 97 produces sampledata.csv2 which can be read in by
+
+ >sampledata <- read.csv2('sampledata2.csv',skip=2)
+
+if the working directory of R was set to the directory where these
+files reside.
diff --git a/inst/doc/sampledata.xls b/inst/doc/sampledata.xls
index 0951ae0..513123b 100644
--- a/inst/doc/sampledata.xls
+++ b/inst/doc/sampledata.xls
Binary files differ
diff --git a/inst/doc/sampledata2.csv b/inst/doc/sampledata2.csv
new file mode 100644
index 0000000..f778dab
--- /dev/null
+++ b/inst/doc/sampledata2.csv
@@ -0,0 +1,33 @@
+Concentration-response data for the Lemna growth test with Substances X and Y;;;;;
+;;;;;
+nr.;substance;dose;unit;fronds;response
+1;Control;0;mg/L;174;1,134782609
+2;Control;0;mg/L;143;0,932608696
+3;Control;0;mg/L;143;0,932608696
+4;Substance X;10;mg/L;147;0,958695652
+5;Substance X;10;mg/L;148;0,965217391
+6;Substance X;10;mg/L;148;0,965217391
+7;Substance X;100;mg/L;63;0,410869565
+8;Substance X;100;mg/L;65;0,423913043
+9;Substance X;100;mg/L;55;0,358695652
+10;Substance X;300;mg/L;20;0,130434783
+11;Substance X;300;mg/L;22;0,143478261
+12;Substance X;300;mg/L;25;0,163043478
+13;Substance X;1000;mg/L;13;0,084782609
+14;Substance X;1000;mg/L;16;0,104347826
+15;Substance X;1000;mg/L;16;0,104347826
+16;Control;0;mg/L;153;0,997826087
+17;Control;0;mg/L;144;0,939130435
+18;Control;0;mg/L;163;1,063043478
+19;Substance Y;10;mg/L;20;0,130434783
+20;Substance Y;10;mg/L;19;0,123913043
+21;Substance Y;10;mg/L;21;0,136956522
+22;Substance Y;100;mg/L;13;0,084782609
+23;Substance Y;100;mg/L;12;0,07826087
+24;Substance Y;100;mg/L;13;0,084782609
+25;Substance Y;300;mg/L;12;0,07826087
+26;Substance Y;300;mg/L;12;0,07826087
+27;Substance Y;300;mg/L;14;0,091304348
+28;Substance Y;1000;mg/L;12;0,07826087
+29;Substance Y;1000;mg/L;12;0,07826087
+30;Substance Y;1000;mg/L;12;0,07826087
diff --git a/man/drplot.Rd b/man/drplot.Rd
index 25b598c..99f77ab 100644
--- a/man/drplot.Rd
+++ b/man/drplot.Rd
@@ -6,7 +6,7 @@
either combined or separately, for one or more substances.
}
\usage{
- drplot(drresults, data, dtype, alpha, path, fileprefix, overlay,
+ drplot(drresults, data, dtype, alpha, ctype, path, fileprefix, overlay,
postscript, png, bw, pointsize, colors, devoff, lpos)
}
\arguments{
@@ -31,6 +31,12 @@
The confidence level, defaulting to 0.95, only used if dtype "conf" has been
chosen.
}
+ \item{ctype}{
+ This argument decides if horizontal lines are drawn to show the scatter of
+ the control values (dose = 0, mean response = 1). Defaults to "none",
+ further allowed values are "std" and "conf" for displaying the standard deviation
+ of the controls or the confidence interval for the mean of the controls.
+ }
\item{path}{
The path where graphic files should be put if any are produced. Defaults
to "./" i.e. the current working directory of R.

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